I only hold the VNs that I'm currently playing and maybe one extra (two if I know they're short) and move my VNs that I'm up to date on over to an external. Keeps my HD less cluttered. I also copy over the RenPy folder and update it each time I play an update. Got into the habit when I had a machine with less space and it just works for me.
Two directories - one for those games whose development is complete, which I've gone through completely, but for one reason or another decided to keep them (I usually delete finished games). The folder is named X_GAMES_COMPLETED, and there are two subdirectories inside: UNITY and RENPY. The meaning, I think, is clear.
And the second folder - X_GAMES_WIP - is for games that I follow the development of (Straitened Times, Bright Past, Amnesia, Summer's Gone, Club Detention, High School Days, Midnight Sin and 3-4 other projects). Same division by engine (Unity and RenPy).
Since I've only saved about 20 or so completed games, it's hard to get confused. So my collection is small.
I have one big folder for the games, and I sort them by "date last modified", which means they're usually sorted in the order that I downloaded them in. As I usually complete games before downloading new ones, this generally makes it pretty easy to handle.
3 HDDs.
One for real games, one for completed AVN and fully translated studio hentai games, one for incomplete AVN and japanese games with ongoing translation.
All 3 have subfolders for main genres like 4x, RPG, Action, Shooter, ... for real games and Lesbian, Loli, Harem, ... for AVN.
Abandoned games end in the dead? folder and every time my diskspace runs low i delete the older ones to free a few TB.